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Nucleic Acids Research 2005 33(6):1741-1748; doi:10.1093/nar/gki316
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Published online 23 March 2005

© The Author 2005. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions{at}oupjournals.org

Article

Conservation versus parallel gains in intron evolution

Alexander V. Sverdlov, Igor B. Rogozin, Vladimir N. Babenko and Eugene V. Koonin*

National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health 8600 Rockville Pike, Bldg 38A, Bethesda, MD 20894, USA

*To whom correspondence should be addressed. Tel: +1 301 435 5913; Fax: +1 301 435 7794; Email: koonin{at}ncbi.nlm.nih.gov

Received January 31, 2005. Revised March 2, 2005. Accepted March 2, 2005.

Orthologous genes from distant eukaryotic species, e.g. animals and plants, share up to 25–30% intron positions. However, the relative contributions of evolutionary conservation and parallel gain of new introns into this pattern remain unknown. Here, the extent of independent insertion of introns in the same sites (parallel gain) in orthologous genes from phylogenetically distant eukaryotes is assessed within the framework of the protosplice site model. It is shown that protosplice sites are no more conserved during evolution of eukaryotic gene sequences than random sites. Simulation of intron insertion into protosplice sites with the observed protosplice site frequencies and intron densities shows that parallel gain can account but for a small fraction (5–10%) of shared intron positions in distantly related species. Thus, the presence of numerous introns in the same positions in orthologous genes from distant eukaryotes, such as animals, fungi and plants, appears to reflect mostly bona fide evolutionary conservation.


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